Related papers: Facilitating Bioinformatics Reproducibility
Rapid advances in computing technology over the past few decades have spurred two extraordinary phenomena in science: large-scale and high-throughput data collection coupled with the creation and implementation of complex statistical…
This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for…
The Coq Platform is a continuously developed distribution of the Coq proof assistant together with commonly used libraries, plugins, and external tools useful in Coq-based formal verification projects. The Coq Platform enables reproducing…
In the rapidly evolving fields of Artificial Intelligence (AI) and Machine Learning (ML), the reproducibility crisis underscores the urgent need for clear validation methodologies to maintain scientific integrity and encourage advancement.…
The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open-source data and tools to propel the field. Despite the…
Computational reproducibility is central to scientific credibility, yet verifying published results at scale remains costly. We develop an AI-assisted workflow for automated full-paper replication -- retrieving materials, reconstructing…
Those seeking to reproduce a computational experiment often need to manually look at the code to see how to build necessary libraries, configure parameters, find data, and invoke the experiment; it is not automatic. Automatic…
A recent study showed that more than 70% of researchers fail to reproduce their peers's experiments and more than half fail to reproduce their own experiments. Obviously, from a perspective of scientific quality this is a more than…
Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducibility and the avoidance of pitfalls. It details practical applications from website management using…
Computational physics increasingly depends on large simulation datasets generated by software that remains under active development for many years. In such settings, reproducibility requires not only well documented data but also explicit…
Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community. Tales are executable research…
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a…
Reproducibility is central to the credibility of scientific findings, yet complete replication studies are costly and infrequent. However, many biological experiments contain internal replication, which is defined as repetition across…
Objective: In this study, we aim to replicate an artefact-based study on software testing to address the gap. We focus on (a) providing a step by step guide of the replication, reflecting on challenges when replicating artefact-based…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
Context: Mining software repositories is a popular means to gain insights into a software project's evolution, monitor project health, support decisions and derive best practices. Tools supporting the mining process are commonly applied by…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…